I am interested nowadays in microarrays, RNA-Seq and genome annotation, GO and pathways. But my goal are to maximize the useful information of each existing experiment. Now I am committing with Bioconductor, you can follow some of my thought in my blog, or in twitter.

... GO.db and org.Hs.eg.db are copies of the GO annotations. GO.db is updated every 6 months with each release of Bioconductor. org.Hs.eg.db is also updated at the same time and using GO.db.
biomaRt connects to the server where the informations is stored, so it will be the most up to date.
If you wan ...

... If they are properly normalized and are the same comparisons on the same biological and experimental background yes. Different methods should agree on the magnitude of the change if not in the value itself, apply common sense. ...

... Sorry but I think I did not understand your comment. Would you mind clarifying why do you say WGCNA will not work? Which metrics for samples and genes are you talking about ? By using gene set enrichment tools I am including gene ontologies. ...

... First, it doesn't make sense to look for biologically interesting modules and then restrict to those which have a similar change. First work with WGCNA all samples that have the same biological state (don't mix condition A and controls), Then evaluate if those modules are coherent between two condi ...

... When you say
> 1000 * 4 (1000 - genes and 4 - logFC value).
Does it mean you have filtered by logFC? You shouldn't do that. See the FAQ of WGCNA.
If you have just 4 samples, then the results will be spurious. WGCNA relays on correlations and you can have quite easily a high correlation with j ...

... Depend what kind of co-expression relation do you want and how pure is. The better it would be to have enough samples per group otherwise the differences between the groups might hide real connections between genes.
1. Yes. It is not unusual to do so. In fact WGCNA has functions to do so (but I w ...

... Gene Set Enrichment methods are designed precisely for that purpose. Having your list of genes (transcripts ) of interest you can apply these methods to the whole list of genes to observe if there is any difference of this group of genes, for instance, it is more expressed in the disease rather than ...